The defender turned Ashley Young's cross into his own net with 20 minutes remaining.
Gunners responded immediately and substitute Emmanuel Adebayor hit the post, but still Arsene Wenger's side were unable to find a way through.
And with time ru
nning out Gabriel Agbonlahor raced through to net Villa's second and stun the home side.
He picked up the ball just inside the Arsenal half and showed great pace before smashing the ball home from 20 yards.
Earlier, Manuel Almunia saved an early penalty to keep Arsenal level at half-time.
The Spanish goalkeeper dived low to his left to save Young's spot-kick to keep it goalless after the Villa player had been brought down by Theo Walcott just inside the box in the 19th minute.
Young only took the kick because Gareth Barry, who normally takes Villa's spot kicks, was injured in the move that led to the penalty being awarded.
Arsenal boss Wenger brought his big guns back after his young side's crushing 3-0 defeat of Wigan in the Carling Cup.
Emmanuel Adebayor, who was an injury doubt ahead of the game, was named on the bench with Nicklas Bendtner starting upfront for an Arsenal team without the suspended Rob van Persie.
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